QC Report - SS2 - Oligo project
Simon Besson-Girard - AGGokce
18/08/2021
- Sequencing
- Alignment
- Average input read length after trimming per sample (bp)
- Uniquely mapped reads during alignment per sample (%)
- Multimapped reads during alignment per sample (%)
- Unmapped due to too short reads during alignment per sample (%)
- Unmapped due to mismatches reads during alignment per sample (%)
- Unmapped-other reads during alignment per sample (%)
- Mismatch Rate per sample
- Sample selection
- Summary of criteria for quality control
Sequencing
Sequencing of 2650 samples, dual-index 100bp paired-end.
Alignment
After further trimming for PHRED quality score, illumina adapter content and alignment against Mouse Genome GRCm38 also called mm10:
Average input read length after trimming per sample (bp)
Uniquely mapped reads during alignment per sample (%)
Multimapped reads during alignment per sample (%)
Unmapped due to too short reads during alignment per sample (%)
Unmapped due to mismatches reads during alignment per sample (%)
Unmapped-other reads during alignment per sample (%)
Mismatch Rate per sample
Sample selection
##
## 1 2 3 4 5 6 7 8 9 10
## 263 429 573 610 250 410 66 10 38 1
Sequencing and Trimming Quality
Mapping Quality
Summary of criteria for quality control
We carefully select the samples that pass the 19 criteria according to the values specified in the table below:
| Criteria | Selection |
|---|---|
| #Genes | >= 1000 & <= 6500 |
| PercentMito | >= 0 & <= 0.006 |
| PercentERCC | >= 0 & <= 0.011 |
| adapter_content | PASS |
| Sequences.flagged.as.poor.quality | 0 |
| sequence_duplication_levels | PASS |
| avg_input_read_length | >= 180 & <= 200 |
| per_base_sequence_quality | PASS |
| sequence_length_distribution | PASS |
| basic_statistics | PASS |
| per_sequence_gc_content | PASS |
| total_reads | >= 20000 & <= 4e+06 |
| per_base_n_content | PASS |
| overrepresented_sequences | PASS |
| per_sequence_quality_scores | PASS |
| uniquely_mapped_percent | >= 68 & <= 100 |
| unmapped_tooshort_percent | >= 0 & <= 17 |
| mismatch_rate | >= 0.15 & <= 0.5 |
| multimapped_percent | >= 2.3 & <= 7.7 |
Quantitative criteria are represented here along with the chosen thresholds. Colour per tissue (GM or WM).
From 2650 single-cells sequenced, we end up with 2538 that passed quantitative QC (seen above).